Assassin Chronicles
by jonty2600
Summary: Captured and Experimented on, Naruto finds himself reliving the memories of his ancestor. With these memories, not only will he uncover the truth behind his capture, but he will also learn the necessary skills to become one of the most infamous Assassins chronicled in the history books.
1. Prologue

**Disclaimer- I do not own** **Naruto** **and** **Assassin's Creed**

* * *

Naruto was unsure of what had occurred during the Chunin exams; he, Sasuke and Sakura were travelling through the Forest of Death, when they encountered a Genin from 'The Village Hidden in the Grass'. The Genin had long smooth black hair and black eyes; he was also wearing a straw hat on his head and was dressed in plain grey garbs with a black polo and pants underneath, a thick purple rope belt tied in a large knot behind his back, blue tomoe-shaped earrings, and shinobi sandals with bandages around his calves. The Genin had separated Naruto from his group and incapacitated him.

As Naruto opened his eyes, he was astonished to find that the environment around him had been converted into a void. Unexpectedly, a flash of light blinded Naruto and the void he was floating in transformed itself into an unfamiliar location; he felt his body change, his face, torso, arms, legs, hands and feet morphed into the limbs of somebody else. His vision was blurred, as if his mind was rejecting his new body. As soon as he was placed into this reality, he returned to his original body and domain.

Gasping for breath, Naruto immediately became upright and looked down at his body; his limbs were as he remembered. He recognised his own torso, arms, legs, hands and feet. He felt his face and breathed a sigh of relief as he confirmed it was his.

"I told you he would be fine" a serpentine voice said.

"You bastards"! Naruto yelled.

"I just saved your life Naruto" the voice said again.

"Saved my life, you kidnapped me, strapped me into this thing"! Naruto said.

"Animus, it's an Animus" the voice continued.

"I don't even know you people, why are you doing this to me"? Naruto asked.

"You have information we need Naruto" the voice informed.

"Information, I'm a Genin, what do you want me to do, save a fucking cat from a tree"? Naruto asked sarcastically.

"Although you don't know Naruto, we have analysed a blood sample we took from you when you were incapacitated; we know your lineage, whether you know it or not, you have got something I want, locked away in that head of yours" the voice notified.

"What do you want from me"? Naruto asked.

"For you to do as your told, the Animus will allow us to locate what we need, once we have it, you will be free to go" the voice said.

"I'm not going back in there" Naruto said.

"Then we'll induce a coma and continue our work, when were done you'll be left to die, truth be told the only reason your still conscious is because this approach saves me time" the voice reported.

"You're insane" Naruto deduced.

"So what is it Naruto, live or die"? The voice asked.

Naruto lay back down and a glass panel rotated over his head. The interface was projected onto the screen, amazing Naruto.

"Whoa, where am I" Naruto asked.

"Inside the Animus" the voice said.

As Naruto turned his head he could see the appearance of the man he was talking to and his assistant. The man had a snake, like appearance; with very pale skin, golden eyes with slitted pupils, purple markings around his eyes and fang-like teeth. He also had pronounced cheekbones and straight waist-length black hair with some locks covering and framing his face or to his shoulders. The assistant was a man who had onyx eyes and ash grey hair, tied in a ponytail; on his face was a pair of black rimmed circular glasses, erringly, this man reminded him of the Genin, Kabuto who took part in the Chunin exams with the other Ninja from 'The Village Hidden in the Leaves'.

"Which is" Naruto asked.

"It's a projector which renders genetic memories in three dimensions" the voice said.

"Genetic memories" Naruto said.

"Seems you will need a tutorial, very well, we will start simple, what is a memory Naruto" the voice asked as an image of a brain appeared on the projector.

"It's the rare collection of a past event" Naruto said.

"Specific to the individual remembering the event" the voice said.

"Yeah sure" Naruto agreed.

The image of a female human body appeared on the screen.

"What if I told you that the human body not only housed an individual memory, but the memories of his ancestor's aswell, genetic memories, if you will; migration, hibernation, reproduction, how do animals know when and where to go, what to do"? The voice asked as the image of an eagle appeared on the screen.

"That's just animal instinct" Naruto supposed.

"Now you're arguing semantics Naruto, whatever you call it, the fact remains, these creatures hold knowledge absent the requisite first-hand experience, I've spent many years trying to understand why, I discovered something most fascinating, our DNA functions as an archive, it contains not only genetic instructions passed down from previous generations, but memories aswell, the memories of our ancestors" the voice concluded.

"And the Animus lets you decode and read these DNA files"? Naruto asked.

"Precisely" The voice said.

The assistant then piped up.

"But there's a problem, this is the specific memory we are trying to access, unfortunately, when we try and open the memory, your mind withdraws, you lack the confidence to step into your ancestors body, that's what happened earlier, you got knocked out of the target memory and pushed back into a more stable state" the assistant said.

"Why"? Naruto asked.

"It's your subconscious, it's resisting; we found similar reactions among patients who undergo hypnosis to relive traumatic events, they can't jump directly into the specific memory, they need to be eased in, even then there can be problems" the assistant informed.

"So how do we fix it"? Naruto asked.

"We find a memory you can synchronise with, and then we move forward from there, you'll get used to it; this is the closest we can get, so it's where we will have to start" the assistant concluded.

* * *

Suddenly, there was a flash of light, and Naruto was placed back inside his ancestor's body. Naruto found himself in a cage; a chain elevated the cage above the ground and kept it from falling down into the depths below. Infront of him was a man, he was dressed in clothing he had never seen before; on his head was an enormous hat of some kind and on his figure, a robe, coloured red and black.

"The box is empty, or should I say incomplete. Where is the rest of it"? The man asked.

Naruto felt like it wasn't the time for him to speak, so he kept silent.

"We know who you are. We know who you were. You've come far for someone who was merely a Concubine" the man continued.

"I will ask you again, Assassin, what is this box? Where did it come from and what is its purpose"? The man demanded.

When Naruto continued not to speak, the man grew even angrier.

"Why continue to resist us? Look around you. No one is coming. We wiped out your order. There is no escape from here" the man stated.

Naruto felt like it was time to speak, but as he opened his mouth, words he did not decide upon were vocalised in a beautiful, feminine voice.

"Why would I want to escape? I am exactly where I want to be" he said.

"Such arrogance, Ma Yongcheng will make you talk"! the man screamed.

"Let him try" Naruto said.

"No wonder your kind fell so far" the man jested.

"My 'Kind' isn't done yet" Naruto said.

As the man turned to leave, Naruto looked down at his ancestor's body. His now female body was outfitted in a red and black robe, with leather boots positioned on his feet. His robe was of an elegant design and had many markings and symbols, sewn into the fabric. Over his robe, he wore a brown, leather tunic, with leather greaves, leather vambraces, leather spaulders and a leather chest guard. Around his waist was a red cloth which held his robe, tighter to his body. At the centre of the red cloth was a symbol he was unfamiliar with. On his wrists were two gauntlets with knives hidden inside them and on his back was a large sword. Naruto pulled at his, soft, neck length, black hair and felt his face; his face was much more feminine, with softer features that his own.

"Who am I"? He said in a womanly voice.

" _You were placed into the body of your ancestor, a member of the Chinese Brotherhood of Assassins known as Shao Jun"_ the serpentine voice informed quietly.


	2. Chapter 1

**Disclaimer- I do not own** **Naruto** **and** **Assassin's Creed**

* * *

"Time to get out of this cage…" Naruto said to himself.

It was strange; when he would speak he would constantly be startled by the sound of his new voice. Naruto ran towards the cage exit and hooked his arms around the top bar of the enclosure. Utilising his new weight, Naruto hammered his feet upon the wooden gateway and broke through it; this caused numerous amounts of debris to be propelled towards the ground below.

Naruto hopped from the cage and landed onto the wooden platform below him. Naruto knew his objectives, he had to rescue the Assassin informant Hong Liwei and Escape the Prison Cells.

As he made his way through the prison, Naruto stopped at the base of a huge barrier, the barrier had numerous wooden boards nailed into it and a copious amount of blood trailing upwards. Naruto sprang onto the barrier and started to scale it, exploiting the boards nailed into it and forming a makeshift ladder. Naruto followed the trail of blood, until he began to hear the loud voices of the guards.

"Huh? Who's there?" a voice asked.

"Stop right there!" another voice demanded.

Naruto could only assume that there was somebody besides himself sneaking through this prison; although, as soon as the two guards spoke, the infiltrator was begging for his life.

"Please, no! Wait…" the voice pleaded.

Naruto could hear the sound of steel on flesh and the agonising cries of a man being brutally murdered.

"I'll let the dogs on the body later" the guard uttered.

After the death of the infiltrator, Naruto continued to make his way through the prison, albeit, more stealthily. He climbed over crates, concealed himself in the shadows and navigated the area. He had to open many gates and scale many barriers in order to escape the prison. As he entered another room, he immediately caused a caged dog to howl, warning its master that he had entered the room.

"What's that?" Naruto heard a voice ask.

In a panic, he began to sprint away from the dog; soaring over ditches and scaling wooden platforms and stockades.

As soon as Naruto escaped the area, he immediately decided that, if he wanted to locate the informant and escape the prison, he would have to locate his ancestor's confiscated inventory. Although, as he was looking, he ran into another guard; before the guard noticed him, Naruto hid in an entryway; he clung to the shadows, effectively hiding himself from the suspicious guard. Naruto slipped past the sentry and exited the area.

In order to distract other guards, Naruto used a whistle to draw the attention of any patrols nearby and lured them away from any exits.

Naruto came across a guard standing idly, he was not turning around, and was not patrolling the area; Naruto decided this would be the best time to examine his weaponry, he slowly walked up behind the guard and grabbed the guards arm, as soon as the he restrained the guard and forced his head downwards, Naruto kicked him in the head, innately using a blade hidden in his boot in order to stab the man in the skull.

Naruto lifted the dead body and hid it in an entryway. Naruto sprinted away from the area and slid underneath an elevated barrier, knowingly entering the area where Shao Jun's rope dart had been stored. He picked the rope dart up, smiling as he did so.

"Good to have you back, my friend…" Naruto whispered.

As soon as he located his rope dart, Naruto ascended up another barrier, where he noticed a guard patrolling the area. He used his hidden blade to stab the sentry, rupturing his stomach in the process. Naruto concealed the body and immediately started leaping from different barriers, in order to locate the missing informant.

After a long search, Naruto had finally found the prison exit. The light from the sun momentarily blinded him, how long had Shao Jun been locked away in this prison?

Naruto crept out of the prison where he was met with two guards who had their backs to him.

"Keep your wits about you" the guard advised.

"And you yours, you're meant to be watching my back" the other guard stated.

"I'll watch yours; just make sure you're watching mine" the other retorted.

Naruto slipped past the guards and entered another area of the prison; as soon as he entered, Naruto was met with a large patrol of guards, although they hadn't noticed him, it would still be difficult to sneak past them.

"A little distraction could help me here" Naruto said to himself.

Naruto whistled, causing a number of the guards to look to his direction, whilst he hid behind a container. Naruto then crawled on his stomach, following the edge of the room, staying out of sight. He made it past the first couple of guardsmen, although there were still some to sneak past. Naruto hid in an entryway, and let the rest of the patrol walk past him, it would seem that they were confused at what the other guards were doing and were investigating what was wrong.

Naruto left this section of the prison and slowly walked out through the exit.

"My revenge can begin now" Naruto said to himself.

Who did Shao Jun want to assassinate, who was she vengeful against? All these questions were brought to Naruto's attention as he left the area.

* * *

Suddenly, a bright light blinded Naruto, as he opened his eyes, he saw an old man infront of him. The man was dressed in rags, and the only weapon he had was a single sword.

"Time to test your sword skills, prepare to defend yourself!" the man commanded.

Naruto blocked one of the old man's strikes; as he looked upwards all he could see was the man's face.

"Remember to look for signs your opponent is about to strike" the man suggested.

Naruto blocked again, causing the man to smile.

"Yes, that's it" the man said.

Naruto moved away from the man and he ordered him to perform another technique.

"This time when you block, perform a rollover" the man demanded.

Naruto blocked his attack, and rolled over the man to get to the other side of him.

"Perfect. This tactic is also good to escape from combat" the man said.

"Well done, Shao Jun. Your training is complete for now".


End file.
